Ligand profile

CHEMBL5270264

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_02423 — tRNA (guanine-N(1)-)-methyltransferase

Via homolog UniProt P0A873 Formula C₁₇H₂₁N₅O₂
pchembl 7.89 ~12.9 nM
Mol. weight 327.39 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL5270264
UniProt (similar protein)
P0A873
pchembl
7.890 (~12.9 nM)
Target protein
KP13_02423

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 327.39 Da
LogP (Crippen) 0.44
H-bond donors 2
H-bond acceptors 5
TPSA 93.25 Ų
Rotatable bonds 4
Aromatic rings 2 / 4
Heavy atoms 24
Fraction sp³ C 0.47
Formula C₁₇H₂₁N₅O₂

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 93.2
  • −1 ≤ LogP ≤ 5 0.44
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 327.4
  • LogP ≤ 5 0.44
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 93.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
NC(=O)c1cnc2c(c1)cc(C1CC1)n2CC(=O)N1CCNCC1
InChI 
InChI=1S/C17H21N5O2/c18-16(24)13-7-12-8-14(11-1-2-11)22(17(12)20-9-13)10-15(23)21-5-3-19-4-6-21/h7-9,11,19H,1-6,10H2,(H2,18,24)
InChIKey 
RYDNISPFFBQXAG-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
ChEMBL
Binding sites
PF01746

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_02423.

PDB 89

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 37

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)